Question: GSEA with mouse RNAseq data
0
gravatar for Alex Gibbs
16 months ago by
Alex Gibbs40
Cardiff University
Alex Gibbs40 wrote:

Hi everyone,

I have had RNAseq performed on mouse samples (12 samples, 4 groups) and have the results ready to plug into Gene Set Enrichment Analysis (GSEA) software.

I notice that there are plenty of human gene sets available on MSigDB, but not many for mouse. I would like to run GSEA with 6 signalling pathway gene sets, but the only ones I can find are for human. Does anyone know if the human signalling pathways are exactly the same as mouse signalling pathways? Or is there a mouse database that I can go onto to download mouse specific signalling pathway gene sets?

Thank you in advance!

Alex

rna-seq • 1.4k views
ADD COMMENTlink modified 11 days ago by Gordon Smyth1.7k • written 16 months ago by Alex Gibbs40

MSigDB pathways are presented as human symbols, but are based on multiple species.

Related discussion: GSEA analysis with Mouse (Please give some comments..)

ADD REPLYlink written 5 weeks ago by igor11k
2
gravatar for Buffo
16 months ago by
Buffo1.8k
Buffo1.8k wrote:

You can use webgestalt, it has a list of organisms (including mouse)

ADD COMMENTlink written 16 months ago by Buffo1.8k
1
gravatar for Gordon Smyth
11 days ago by
Gordon Smyth1.7k
Australia
Gordon Smyth1.7k wrote:

We created a mouse version of the MSigDB, available from http://bioinf.wehi.edu.au/MSigDB/

ADD COMMENTlink modified 9 days ago • written 11 days ago by Gordon Smyth1.7k
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